OK, but then all of a sudden, all my virtual hosts are down and unavailable. Restarting Apache through cli first gives me a no pid file running when trying to shut down and then it starts again. So cli manually, apache starts, but through the SIGWINCH ispconfig is calling, it does not start up again.

Your Linux system should allow it to use "/etc/init.d/apache2 reload" which ispconfig is using. So if it fails on your system, you might have to modify the apache start script so that it does a restart too when the reload parameter is used.